Pre-visualization of the normalized count data before any differential analysis
Warning message in is.na(x[[i]]): “is.na() applied to non-(list or vector) of type 'environment'”
========================================================================== * * Package WGCNA 1.63 loaded. * * Important note: It appears that your system supports multi-threading, * but it is not enabled within WGCNA in R. * To allow multi-threading within WGCNA with all available cores, use * * allowWGCNAThreads() * * within R. Use disableWGCNAThreads() to disable threading if necessary. * Alternatively, set the following environment variable on your system: * * ALLOW_WGCNA_THREADS=<number_of_processors> * * for example * * ALLOW_WGCNA_THREADS=4 * * To set the environment variable in linux bash shell, type * * export ALLOW_WGCNA_THREADS=4 * * before running R. Other operating systems or shells will * have a similar command to achieve the same aim. * ========================================================================== Allowing multi-threading with up to 4 threads. [1] "preparing gene to GO mapping data..." [1] "preparing IC data..." [1] "preparing gene to GO mapping data..." [1] "preparing IC data..." [1] "preparing gene to GO mapping data..." [1] "preparing IC data..."
| GF_104w_F_1_2 | GF_104w_F_2_2 | GF_104w_F_3_2 | GF_104w_M_1_2 | GF_104w_M_2_2 | GF_52w_M_1_2 | GF_52w_M_2_2 | GF_52w_M_3_2 | GF_52w_M_4_2 | GF_8w_M_1_2 | ⋯ | SPF_104w_M_14_2 | SPF_8w_F_1_2 | SPF_8w_F_3_2 | SPF_8w_F_4_2 | SPF_8w_F_5_2 | GF_8w_F_1_2 | GF_8w_F_2_2 | GF_8w_F_3_2 | GF_8w_F_4_2 | GF_8w_F_5_2 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 0610005C13Rik | 0.0000 | 0.00000 | 0.0000 | 1.768593 | 1.259244 | 0.8418979 | 4.942785 | 5.603216 | 7.231584 | 8.47277 | ⋯ | 5.28524 | 3.500355 | 2.112002 | 2.602398 | 0.00000 | 18.24998 | 0.00000 | 2.025447 | 5.268672 | 0.00000 |
| Erg28 | 868.4015 | 749.64927 | 910.3535 | 886.064952 | 992.913601 | 508.5063502 | 530.855142 | 514.375197 | 738.344705 | 603.98749 | ⋯ | 692.36648 | 763.077332 | 744.480801 | 908.237050 | 957.79030 | 898.54336 | 682.26034 | 612.697796 | 593.252445 | 809.27852 |
| 0610009B22Rik | 1021.3276 | 1169.19730 | 1180.9991 | 1224.750457 | 1558.313990 | 1038.9020466 | 876.850113 | 1016.423320 | 877.914273 | 948.95029 | ⋯ | 1206.79653 | 1268.295198 | 1164.769254 | 1295.994415 | 1446.89758 | 1040.24912 | 1020.67017 | 1142.352254 | 959.952003 | 1094.00091 |
| 0610009L18Rik | 28.2185 | 36.20465 | 18.2253 | 20.338816 | 38.406931 | 31.9921214 | 26.691041 | 22.412863 | 4.338950 | 61.73018 | ⋯ | 45.80542 | 42.004257 | 45.408049 | 102.794738 | 72.02239 | 48.30878 | 19.58642 | 11.139960 | 45.310578 | 24.36813 |
| 0610009O20Rik | 217.5555 | 278.98879 | 266.0893 | 226.379868 | 271.996624 | 299.7156634 | 349.949200 | 395.587025 | 309.511786 | 360.69794 | ⋯ | 178.81730 | 274.194454 | 252.384272 | 227.709862 | 184.89330 | 231.88216 | 158.86764 | 271.409933 | 304.529230 | 269.33199 |
| 0610010B08Rik | 0.0000 | 0.00000 | 0.0000 | 0.000000 | 0.000000 | 0.0000000 | 0.000000 | 0.000000 | 0.000000 | 0.00000 | ⋯ | 0.00000 | 0.000000 | 0.000000 | 0.000000 | 0.00000 | 0.00000 | 0.00000 | 0.000000 | 0.000000 | 0.00000 |
pickSoftThreshold: will use block size 4378. pickSoftThreshold: calculating connectivity for given powers... ..working on genes 1 through 4378 of 10219 ..working on genes 4379 through 8756 of 10219 ..working on genes 8757 through 10219 of 10219 Power SFT.R.sq slope truncated.R.sq mean.k. median.k. max.k. 1 2 0.144 -0.617 0.901 644.0000 6.20e+02 1390.00 2 4 0.691 -1.460 0.964 114.0000 9.21e+01 438.00 3 6 0.783 -1.840 0.970 31.1000 1.94e+01 198.00 4 8 0.790 -2.020 0.962 11.0000 5.03e+00 106.00 5 10 0.832 -1.990 0.985 4.6100 1.49e+00 63.10 6 12 0.851 -1.960 0.988 2.1900 4.90e-01 40.10 7 14 0.876 -1.890 0.988 1.1500 1.72e-01 26.70 8 16 0.886 -1.820 0.971 0.6430 6.43e-02 18.40 9 18 0.899 -1.780 0.970 0.3830 2.50e-02 13.60 10 20 0.882 -1.770 0.946 0.2400 1.02e-02 10.40 11 22 0.917 -1.720 0.984 0.1560 4.29e-03 8.11 12 24 0.902 -1.700 0.962 0.1050 1.86e-03 6.46 13 26 0.408 -2.230 0.416 0.0724 8.32e-04 5.23 14 28 0.416 -2.190 0.427 0.0514 3.76e-04 4.28 15 30 0.931 -1.630 0.984 0.0372 1.74e-04 3.55
Parameters for network construction
ERROR while rich displaying an object: Error in sprintf(wrap, header, body): 'fmt' length exceeds maximal format length 8192
Traceback:
1. FUN(X[[i]], ...)
2. tryCatch(withCallingHandlers({
. rpr <- mime2repr[[mime]](obj)
. if (is.null(rpr))
. return(NULL)
. prepare_content(is.raw(rpr), rpr)
. }, error = error_handler), error = outer_handler)
3. tryCatchList(expr, classes, parentenv, handlers)
4. tryCatchOne(expr, names, parentenv, handlers[[1L]])
5. doTryCatch(return(expr), name, parentenv, handler)
6. withCallingHandlers({
. rpr <- mime2repr[[mime]](obj)
. if (is.null(rpr))
. return(NULL)
. prepare_content(is.raw(rpr), rpr)
. }, error = error_handler)
7. mime2repr[[mime]](obj)
8. repr_latex.matrix(obj)
9. repr_matrix_generic(obj, sprintf("\\begin{tabular}{%s}\n%%s%%s\\end{tabular}\n",
. cols), "%s\\\\\n\\hline\n", " &", " %s &", "%s", "\t%s\\\\\n",
. "%s &", " %s &", escape_fun = latex_escape_vec, ...)
10. sprintf(wrap, header, body)
| Erg28 | 0610009B22Rik | 0610009L18Rik | 0610009O20Rik | 0610010F05Rik | 0610010K14Rik | Mettl26 | 0610012G03Rik | 0610030E20Rik | 0610037L13Rik | ⋯ | Zw10 | Zwint | Zxda | Zxdb | Zxdc | Zyg11b | Zyx | Zzef1 | Zzz3 | Hikeshi | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| GF_104w_F_1_2 | 868.4015 | 1021.328 | 28.21850 | 217.5555 | 411.4439 | 1351.757 | 283.0953 | 693.6289 | 899.3508 | 449.6754 | ⋯ | 618.0761 | 1471.913 | 297.6596 | 130.1692 | 923.9282 | 1333.552 | 2864.633 | 396.8795 | 752.7967 | 668.1412 |
| GF_104w_F_2_2 | 749.6493 | 1169.197 | 36.20465 | 278.9888 | 461.0769 | 1516.336 | 207.6443 | 686.8236 | 759.2329 | 526.0323 | ⋯ | 797.5672 | 1539.763 | 243.8490 | 198.0607 | 981.7850 | 1340.637 | 3358.514 | 364.1762 | 597.3768 | 703.8610 |
| GF_104w_F_3_2 | 910.3535 | 1180.999 | 18.22530 | 266.0893 | 288.8709 | 1852.601 | 222.3486 | 868.4353 | 540.3800 | 444.6972 | ⋯ | 731.7456 | 1375.099 | 153.0925 | 171.3178 | 922.1999 | 1181.910 | 3058.205 | 209.5909 | 644.2642 | 770.9300 |
| GF_104w_M_1_2 | 886.0650 | 1224.750 | 20.33882 | 226.3799 | 278.5534 | 1551.056 | 190.1237 | 823.2799 | 525.2720 | 607.5116 | ⋯ | 466.9085 | 1752.675 | 172.4378 | 344.8756 | 683.5611 | 1295.494 | 2789.955 | 261.7517 | 944.4285 | 687.9826 |
| GF_104w_M_2_2 | 992.9136 | 1558.314 | 38.40693 | 271.9966 | 304.1073 | 1911.532 | 243.0340 | 778.8422 | 707.6949 | 586.8075 | ⋯ | 878.3224 | 1957.494 | 147.9611 | 249.3302 | 1003.6172 | 1205.726 | 2819.446 | 200.8494 | 785.1384 | 583.6594 |
| GF_52w_M_1_2 | 508.5064 | 1038.902 | 31.99212 | 299.7157 | 392.3244 | 1173.606 | 182.6919 | 589.3286 | 1047.3210 | 621.3207 | ⋯ | 768.6528 | 1397.551 | 287.9291 | 275.3006 | 924.4039 | 1674.535 | 2206.614 | 749.2892 | 1163.5029 | 493.3522 |
Calculating module eigengenes block-wise from all genes
Flagging genes and samples with too many missing values...
..step 1
....pre-clustering genes to determine blocks..
Projective K-means:
..k-means clustering..
..merging smaller clusters...
Block sizes:
gBlocks
1 2 3
4997 4015 1207
..Working on block 1 .
TOM calculation: adjacency..
..will use 4 parallel threads.
Fraction of slow calculations: 0.000000
..connectivity..
..matrix multiplication (system BLAS)..
..normalization..
..done.
..saving TOM for block 1 into file norm_genes_TOM-block.1.RData
....clustering..
....detecting modules..
....calculating module eigengenes..
....checking kME in modules..
..Working on block 2 .
TOM calculation: adjacency..
..will use 4 parallel threads.
Fraction of slow calculations: 0.000000
..connectivity..
..matrix multiplication (system BLAS)..
..normalization..
..done.
..saving TOM for block 2 into file norm_genes_TOM-block.2.RData
....clustering..
....detecting modules..
....calculating module eigengenes..
....checking kME in modules..
..Working on block 3 .
TOM calculation: adjacency..
..will use 4 parallel threads.
Fraction of slow calculations: 0.000000
..connectivity..
..matrix multiplication (system BLAS)..
..normalization..
..done.
..saving TOM for block 3 into file norm_genes_TOM-block.3.RData
....clustering..
....detecting modules..
No modules detected in block 3
..reassigning 1 genes from module 1 to modules with higher KME.
..reassigning 1 genes from module 9 to modules with higher KME.
..reassigning 3 genes from module 10 to modules with higher KME.
..reassigning 3 genes from module 11 to modules with higher KME.
..reassigning 1 genes from module 14 to modules with higher KME.
..merging modules that are too close..
mergeCloseModules: Merging modules whose distance is less than 0.2
Calculating new MEs...
0 1 2 3 4 5 6 7 8 9 10 11 8786 446 260 191 95 93 86 62 56 53 49 42
TOM calculation: adjacency.. ..will use 4 parallel threads. Fraction of slow calculations: 0.000000 ..connectivity.. ..matrix multiplication (system BLAS).. ..normalization.. ..done.
| 0610030E20Rik | 1600020E01Rik | Zfp974 | 1700094D03Rik | Lrmda | 1810026B05Rik | Ndufaf8 | 2010107E04Rik | 2210016L21Rik | 2310033P09Rik | ⋯ | Zmpste24 | Zmym6 | Znhit2 | Znrd1 | Znrf1 | Znrf2 | Zrsr2 | Zscan26 | Zswim8 | Zzef1 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 0610030E20Rik | 1 | 1 | 0 | 0 | 0 | 1 | 0 | 0 | 0 | 0 | ⋯ | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 1 | 0 | 0 |
| 1600020E01Rik | 1 | 1 | 0 | 1 | 0 | 1 | 0 | 0 | 0 | 0 | ⋯ | 0 | 1 | 0 | 0 | 1 | 0 | 0 | 1 | 1 | 0 |
| Zfp974 | 0 | 0 | 1 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | ⋯ | 0 | 0 | 1 | 0 | 0 | 0 | 0 | 0 | 0 | 0 |
| 1700094D03Rik | 0 | 1 | 0 | 1 | 0 | 1 | 0 | 0 | 0 | 0 | ⋯ | 0 | 1 | 0 | 0 | 0 | 0 | 0 | 1 | 0 | 0 |
| Lrmda | 0 | 0 | 0 | 0 | 1 | 0 | 0 | 0 | 0 | 0 | ⋯ | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 |
| 1810026B05Rik | 1 | 1 | 0 | 1 | 0 | 1 | 0 | 0 | 0 | 0 | ⋯ | 0 | 1 | 0 | 0 | 1 | 0 | 0 | 1 | 1 | 0 |
[1] 1
Warning message in grep(txdbPattern, installedPackages): “argument 'pattern' has length > 1 and only the first element will be used”Warning message in pcls(G): “initial point very close to some inequality constraints”Fetching GO annotations... For 3129 genes, we could not find any categories. These genes will be excluded. To force their use, please run with use_genes_without_cat=TRUE (see documentation). This was the default behavior for version 1.15.1 and earlier. Calculating the p-values... 'select()' returned 1:1 mapping between keys and columns
category over_represented_pvalue under_represented_pvalue numDEInCat
3120 GO:0006325 1.382659e-17 1 59
5992 GO:0016569 1.359305e-14 1 48
4831 GO:0010467 2.437477e-13 1 177
5993 GO:0016570 7.247069e-13 1 40
9691 GO:0034641 1.068901e-12 1 194
14183 GO:0051171 1.176385e-12 1 156
numInCat term ontology
3120 676 chromatin organization BP
5992 483 chromatin modification BP
4831 4700 gene expression BP
5993 380 histone modification BP
9691 5477 cellular nitrogen compound metabolic process BP
14183 3764 regulation of nitrogen compound metabolic process BP
[1] 2
Warning message in grep(txdbPattern, installedPackages): “argument 'pattern' has length > 1 and only the first element will be used”Warning message in pcls(G): “initial point very close to some inequality constraints”Fetching GO annotations... For 3129 genes, we could not find any categories. These genes will be excluded. To force their use, please run with use_genes_without_cat=TRUE (see documentation). This was the default behavior for version 1.15.1 and earlier. Calculating the p-values... 'select()' returned 1:1 mapping between keys and columns
category over_represented_pvalue under_represented_pvalue numDEInCat
9894 GO:0034976 3.199595e-08 1.0000000 16
3466 GO:0006810 7.546882e-08 1.0000000 94
5353 GO:0015031 9.893192e-08 1.0000000 50
14223 GO:0051234 2.388994e-07 1.0000000 95
12344 GO:0045184 4.804425e-07 0.9999999 52
13409 GO:0048193 9.212631e-07 0.9999998 14
numInCat term ontology
9894 201 response to endoplasmic reticulum stress BP
3466 4060 transport BP
5353 1638 protein transport BP
14223 4209 establishment of localization BP
12344 1798 establishment of protein localization BP
13409 186 Golgi vesicle transport BP
[1] 3
Warning message in grep(txdbPattern, installedPackages): “argument 'pattern' has length > 1 and only the first element will be used”Fetching GO annotations... For 3129 genes, we could not find any categories. These genes will be excluded. To force their use, please run with use_genes_without_cat=TRUE (see documentation). This was the default behavior for version 1.15.1 and earlier. Calculating the p-values... 'select()' returned 1:1 mapping between keys and columns
category over_represented_pvalue under_represented_pvalue numDEInCat
3466 GO:0006810 3.075944e-24 1 81
14223 GO:0051234 3.707310e-24 1 82
14189 GO:0051179 8.161022e-24 1 91
14937 GO:0055114 4.936305e-22 1 43
12757 GO:0046034 4.491817e-20 1 24
4464 GO:0009167 2.443053e-19 1 24
numInCat term ontology
3466 4060 transport BP
14223 4209 establishment of localization BP
14189 5314 localization BP
14937 878 oxidation-reduction process BP
12757 180 ATP metabolic process BP
4464 205 purine ribonucleoside monophosphate metabolic process BP
[1] 4
Warning message in grep(txdbPattern, installedPackages): “argument 'pattern' has length > 1 and only the first element will be used”Warning message in pcls(G): “initial point very close to some inequality constraints”Fetching GO annotations... For 3129 genes, we could not find any categories. These genes will be excluded. To force their use, please run with use_genes_without_cat=TRUE (see documentation). This was the default behavior for version 1.15.1 and earlier. Calculating the p-values... 'select()' returned 1:1 mapping between keys and columns
[1] category over_represented_pvalue under_represented_pvalue [4] numDEInCat numInCat term [7] ontology <0 rows> (or 0-length row.names) [1] 5
Warning message in grep(txdbPattern, installedPackages): “argument 'pattern' has length > 1 and only the first element will be used”Warning message in pcls(G): “initial point very close to some inequality constraints”Fetching GO annotations... For 3129 genes, we could not find any categories. These genes will be excluded. To force their use, please run with use_genes_without_cat=TRUE (see documentation). This was the default behavior for version 1.15.1 and earlier. Calculating the p-values... 'select()' returned 1:1 mapping between keys and columns
[1] category over_represented_pvalue under_represented_pvalue [4] numDEInCat numInCat term [7] ontology <0 rows> (or 0-length row.names) [1] 6
Warning message in grep(txdbPattern, installedPackages): “argument 'pattern' has length > 1 and only the first element will be used”Warning message in pcls(G): “initial point very close to some inequality constraints”Fetching GO annotations... For 3129 genes, we could not find any categories. These genes will be excluded. To force their use, please run with use_genes_without_cat=TRUE (see documentation). This was the default behavior for version 1.15.1 and earlier. Calculating the p-values... 'select()' returned 1:1 mapping between keys and columns
[1] category over_represented_pvalue under_represented_pvalue [4] numDEInCat numInCat term [7] ontology <0 rows> (or 0-length row.names) [1] 7
Warning message in grep(txdbPattern, installedPackages): “argument 'pattern' has length > 1 and only the first element will be used”Fetching GO annotations... For 3129 genes, we could not find any categories. These genes will be excluded. To force their use, please run with use_genes_without_cat=TRUE (see documentation). This was the default behavior for version 1.15.1 and earlier. Calculating the p-values... 'select()' returned 1:1 mapping between keys and columns
category over_represented_pvalue under_represented_pvalue numDEInCat
1051 GO:0002376 0 1 39
1089 GO:0002443 0 1 12
4623 GO:0009615 0 1 14
9394 GO:0034097 0 1 16
14446 GO:0051607 0 1 12
16685 GO:0071345 0 1 15
numInCat term ontology
1051 2150 immune system process BP
1089 290 leukocyte mediated immunity BP
4623 306 response to virus BP
9394 553 response to cytokine BP
14446 268 defense response to virus BP
16685 458 cellular response to cytokine stimulus BP
[1] 8
Warning message in grep(txdbPattern, installedPackages): “argument 'pattern' has length > 1 and only the first element will be used”Fetching GO annotations... For 3129 genes, we could not find any categories. These genes will be excluded. To force their use, please run with use_genes_without_cat=TRUE (see documentation). This was the default behavior for version 1.15.1 and earlier. Calculating the p-values... 'select()' returned 1:1 mapping between keys and columns
category over_represented_pvalue under_represented_pvalue numDEInCat
15 GO:0000028 0 1 7
936 GO:0002181 0 1 9
3176 GO:0006412 0 1 40
3250 GO:0006518 0 1 40
3463 GO:0006807 0 1 46
3972 GO:0008152 0 1 46
numInCat term ontology
15 19 ribosomal small subunit assembly BP
936 49 cytoplasmic translation BP
3176 597 translation BP
3250 738 peptide metabolic process BP
3463 5797 nitrogen compound metabolic process BP
3972 9802 metabolic process BP
[1] 9
Warning message in grep(txdbPattern, installedPackages): “argument 'pattern' has length > 1 and only the first element will be used”Warning message in pcls(G): “initial point very close to some inequality constraints”Fetching GO annotations... For 3129 genes, we could not find any categories. These genes will be excluded. To force their use, please run with use_genes_without_cat=TRUE (see documentation). This was the default behavior for version 1.15.1 and earlier. Calculating the p-values... 'select()' returned 1:1 mapping between keys and columns
[1] category over_represented_pvalue under_represented_pvalue [4] numDEInCat numInCat term [7] ontology <0 rows> (or 0-length row.names) [1] 10
Warning message in grep(txdbPattern, installedPackages): “argument 'pattern' has length > 1 and only the first element will be used”Warning message in pcls(G): “initial point very close to some inequality constraints”Fetching GO annotations... For 3129 genes, we could not find any categories. These genes will be excluded. To force their use, please run with use_genes_without_cat=TRUE (see documentation). This was the default behavior for version 1.15.1 and earlier. Calculating the p-values... 'select()' returned 1:1 mapping between keys and columns
[1] category over_represented_pvalue under_represented_pvalue [4] numDEInCat numInCat term [7] ontology <0 rows> (or 0-length row.names) [1] 11
Warning message in grep(txdbPattern, installedPackages): “argument 'pattern' has length > 1 and only the first element will be used”Warning message in pcls(G): “initial point very close to some inequality constraints”Fetching GO annotations... For 3129 genes, we could not find any categories. These genes will be excluded. To force their use, please run with use_genes_without_cat=TRUE (see documentation). This was the default behavior for version 1.15.1 and earlier. Calculating the p-values... 'select()' returned 1:1 mapping between keys and columns
category over_represented_pvalue under_represented_pvalue numDEInCat
14458 GO:0051641 1.957635e-06 0.9999997 16
9673 GO:0034613 1.885418e-05 0.9999969 12
3938 GO:0008104 1.921928e-05 0.9999962 15
16390 GO:0070727 2.034254e-05 0.9999966 12
numInCat term ontology
14458 2158 cellular localization BP
9673 1444 cellular protein localization BP
3938 2274 protein localization BP
16390 1455 cellular macromolecule localization BP
[1] "1: 12 - 2.69058295964126%" [1] "2: 14 - 5.38461538461539%" [1] "3: 6 - 3.1413612565445%" [1] "4: 1 - 1.05263157894737%" [1] "5: 1 - 1.0752688172043%" [1] "6: 4 - 4.65116279069767%" [1] "7: 2 - 3.2258064516129%" [1] "8: 2 - 3.57142857142857%" [1] "9: 2 - 3.77358490566038%" [1] "10: 0 - 0%" [1] "11: 0 - 0%"
Module 1: chromatine/chromosome organization/RNA metabolic process
Module 2: response to endoplasmic reticulum stress/transport
Module 3: metabolic process (ATP, ribonucleoside)
Module 4
Module 5
Module 6: metabolic process (primary, cellular)
Module 7: immune system
Module 8: translation/rRNA
Module 9
Module 10: organelle
Module 11: localization